JAL-1517 source formatting

[jalview.git] / src / jalview / ws / SequenceFetcher.java

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index ad7b578..caf5b5e 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -52,6 +52,7 @@ public class SequenceFetcher extends ASequenceFetcher
   {
     this(true);
   }
+
   public SequenceFetcher(boolean addDas)
   {
     addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
@@ -66,7 +67,8 @@ public class SequenceFetcher extends ASequenceFetcher
     // PFAM
     addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
-    if (addDas) {
+    if (addDas)
+    {
       registerDasSequenceSources();
     }
   }
@@ -224,13 +226,14 @@ public class SequenceFetcher extends ASequenceFetcher
             + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
             + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
             + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
-    boolean withDas=true;
-    if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+    boolean withDas = true;
+    if (argv != null && argv.length > 0
+            && argv[0].toLowerCase().startsWith("-nodas"))
     {
-      withDas=false;
-      String targs[] = new String[argv.length-1];
+      withDas = false;
+      String targs[] = new String[argv.length - 1];
       System.arraycopy(argv, 1, targs, 0, targs.length);
-      argv=targs;
+      argv = targs;
     }
     if (argv != null && argv.length > 0)
     {
@@ -244,11 +247,13 @@ public class SequenceFetcher extends ASequenceFetcher
           AlignmentI al = null;
           try
           {
-            al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
+            al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
+                    .getTestQuery());
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+            System.err.println("Error when retrieving "
+                    + (argv.length > 1 ? argv[1] : sp.getTestQuery())
                     + " from " + argv[0] + "\nUsage: " + usage);
           }
           SequenceI[] prod = al.getSequencesArray();